Introduction to integrated methods in the vegetable garden
Rhizosphere, mychorizae and suppressive soils
Chapter : Crop soil
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⇒ Rhizosphere, mycorrhizae and suppressive soils.
Introduction to integrated methods in the vegetable garden
Chapter : Crop soil
Previous or next articles ; click on a title to go to the page
⇒ Rhizosphere, mycorrhizae and suppressive soils.
Plants host a very large number of organisms inside or on the surface of their tissues. These organisms form the plant's microbiota. Certain micro-organisms called endophytes (which live in a plant for at least part of its life), some of which thrive in the root zone, are of major importance to plants. Knowledge about their diversity and ecological functions is still incomplete. Epiphytic populations live on the surface or near the roots. The rhizosphere refers to the zone where soil micro-organisms are most concentrated specifically influenced by the root system with a high level of taxonomic diversity.
Lhe phyllosphere contains the micro-organisms that live on a plant above the soil. If nutrient resources on the leaf surface are limited, the epiphytic microbiota is thought to be important in protecting plants against leaf diseases.
Endophytes have only recently been discovered, although they are ubiquitous in plants. It is estimated that most plants live in symbiosis with endophytes that provide them with various services related to nutrient uptake and their ability to defend themselves against pests and even physical stresses (such as drought).
Bacteria associated with plants are classified into beneficial and deleterious groups according to their effects on plant growth. Beneficial soil bacteria are generally referred to as Plant Growth Promoting Rhizobacteria (PGPR). Extracellular PGPRs act on the root surface (known as the rhizoplane) or in the spaces between the cells of the root cortex, while intracellular PGPRs refer to bacteria that secrete substances that target root cells to form specialised nodules that house these PGPRs (such as rhizobium that fix atmospheric nitrogen).
In the rhizosphere, microbial activity is stimulated by organic compounds secreted by the roots. The composition of these root exudates varies greatly from one plant species to another. These root exudates contain different substrates (carbohydrates, mineral salts, amino acids ....) providing a rich source of energy and nutrients for the bacteria. It is estimated that about 5-30% of the substances synthesised by plants are transferred to micro-organisms in the rhizosphere via the roots.
This process is called rhizodeposition. The micro-organisms that colonise the rhizosphere are called rhizobacteria. It is known that only 1-2% of soil bacteria are involved in this process (1), but the number of bacteria around plant roots is usually 10-100 times higher than in the non-root explored soil.
This nurturing environment gives an advantage to micro-organisms that have the potential to multiply rapidly. Fungal growth is also stimulated, but to a lesser extent. It should be noted that root exudates can inhibit the germination of certain competing plants
Root exudates can favour the emergence of pathogenic soil-borne micro-organisms (a) such as agrobacterium tumefaciens responsible for crown gall (2), Erwinia which are pathogens of certain fruit trees (fire blight) or vegetable plants, or the fungus Plasmodiophora brassicae responsible for cabbage looper. Plasmodiophora brassicae persists in the soil in the form of oospores (b). These pathogenic micro-organisms, if not controlled by rotation and solarisation, can have important economic consequences.
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Indirect plant growth promotion occurs when RFCPs modify or prevent the deleterious effects of one or more plant pathogens. This can occur by inducing resistance to the pathogens in the plant or when the RFCPs themselves produce antagonistic substances. These RFCPs are also considered to be safeners because of their ability to antagonise pathogen activity through various processes (antibiotic production, food competition, etc.). They are at the origin of the properties of "resistant" soils studied in more detail in the article below: "Suppressive soils".
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Direct promotion of plant growth by RFCPs consists either in supplying the plant with a compound synthesised by a bacterium, e.g. phytohormones (auxin, gibberellin, etc.), or, as in the case of azotobacteria, in promoting the acquisition of certain nutrients such as atmospheric nitrogen. Some bacteria promote the extraction of iron from mineral complexes by siderophores (c), or, like Bacillus Amyloliquefaciens, produce the solubilisation of phosphates. Other bacteria stimulate root growth.
PCRFs can intervene in plant development by using several of these direct and indirect mechanisms. Mycorrhizal fungi known to provide phosphorus to plants are also able to enhance their natural defences against abiotic stresses or pests. The filamentous fungus Coniothyrium Minitans stimulates root development and destroys the sclerotia of Sclerotinia, the dreaded sunflower pest. Recent studies have demonstrated the suppression of soil-borne fungal pathogens by fluorescent pseudomonads that release iron-chelating siderophores (in iron-poor soils), making iron inaccessible to these fungal pathogens (2).
All these data show that it is important not to unbalance the rhizosphere with toxic substances: discharge of industrial or domestic residues; indiscriminate use of synthetic or organic residual pesticides such as copper-containing compounds...
The major influences that micro-organisms in the rhizosphere exert on plants are now becoming important tools for protecting plant health and promoting plant growth. In recent years, research has been undertaken on RFCPs in the hope that they will complement or replace agrochemicals (fertilisers and pesticides) by various mechanisms involved in humus production, recycling of mineral nutrients, reinforcement of natural plant defences and biological control of pests. The results obtained and their limitations are presented here.
a) Telluric: refers to bacteria that live naturally in the soil.
b) A type of highly resistant sexual spore that forms as a result of fertilisation of an oosphere (female gamete in plants).
c) Siderophores: small peptide molecules with functional groups capable of producing chelated iron. Hundreds of siderophores have been identified in cultivable micro-organisms, some of which are widely used by different micro-organisms, while others are specific to certain species.
Fungi living in the rhizosphere are able to form symbiotic structures with plant roots called mycorrhizae. It is estimated that 90% of plant species are mycorrhized. Ectomycorrhizal complexes are common in plants and often incorporate specific endophytic bacteria. Mycorrhizal fungi help their host plants to acquire mineral nutrients from the soil, including phosphorus and nitrogen. In return, these fungi receive sugars. This mutualistic association allows a better absorption of trace elements that are not very mobile in the soil. The transfer of sugars to the mycorrhizal fungi helps to increase the soil's carbon reserve. When certain elements are present in large quantities and become a toxic threat, mycorrhization can play a role in protecting the plant by strongly retaining these elements
There are three types of fungi capable of forming these associative structures, including the Arbuscular Mycorrhizal Fungi (a) (AMF), also known as glomeromycetes. AMFs have brush-like structures which are the origin of the term "arbuscular". 80% of terrestrial plants are associated with C.M.A. and the latter cover about 20-30% of the soil microbial biomass.
Almost all cultivated plants are involved in mycorrhizal symbiosis, except for certain members of the brassica family (formerly known as crucifers such as cabbage and cauliflower), or the mustard family such as canola and crambe. This association between plants and fungi allows a greater exploration of the soil volume by the mycelium of the fungi forming filamentous structures called hyphae, in areas not accessible by the roots of the plants. For this reason, one should never forget to water or apply supplementary fertilisers beyond the apparent root zone, just as one should never apply residual antifungals, which would have a harmful impact in the zone explored by mycorrhizae sensitive to these antifungals.
The filamentous elements of MACs present in significant quantities in soils have the property of reinforcing the aggregation of soil constituents by secreting a hydrophobic glycoprotein bound to 9% iron and called glomalin. Glomalin contains 30-40% carbon and it is estimated that about 1/3 of the carbon in the soil is in the form of glomalin (6 - 7). Glomalin binds to different mineral particles (clay, silt and sand) to form stable agglomerates which facilitate the absorption of nutrients by the hyphae of the fungi. Clay-humus aggregates are more stabilised when the soil contains glomalin, which acts as a kind of glue.
Glomalin is said to be unique among soil components for its strength and stability. Other soil components that contain carbon and nitrogen are rapidly decomposed by soil microbes, which is not the case for glomalin, which has an estimated lifespan of 7 to 42 years depending on local conditions.
Cultivated soils that have the property of producing resistance to certain soil-borne diseases
Plant-protecting rhizobacteria are at the origin of so-called "resistant" or "suppressive" soils, in which the development of one or more fungal or bacterial soilborne disease agents is limited despite their presence in the soil. A soil in which certain diseases are easily expressed is called "susceptible" or "permissive". As far as vegetable crops are concerned, there is a good example of a resistant soil in the PACA region of French: melons grown in the Châteaurenard region, where the alluvium of the Durance predominates, are known to be little affected by vascular fusariosis. Other examples include soils that are suppressive to damping-off in beets caused by the fungus Rhizoctonia solani, and for field crops, soils that are suppressive to scald in wheat caused by a fungus of the Gaeumannomyces family, or to black rot in tobacco roots caused by Tielaviopsis basicola.
Suppressive soils, which are not very common, have been the subject of research for more than twenty years in order to understand the causes of this resistance to the development of certain diseases. The factors are complex and not all are known. The addition of organic matter in the form of composts or even sewage sludge containing a lot of bacterial walls (which favour the development of actinomycetes) reduces the virulence of certain parasites living in the soil, such as rhizoctone fungi or the fungus that causes damping-off (pythium). Researchers have also found that resistance to Pseudomonas solanacearum, a bacterial wilt agent, is linked to the presence of certain types of clay. The maintenance of the pathogen L Moocytogen in the soil is increased 3.5-fold when soil microbial biodiversity is reduced by 30% (8).
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Either by antagonism by producing hydrolytic enzymes, such as proteases, chitinases, lipases, lucanases, which can lyse the cells of pathogenic fungi, or antibiotics and bacteriocides (b) which interfere with the growth or metabolic activities of other micro-organisms.
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Either by interference by reducing the action of molecules involved in the growth of pathogenic organisms.
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Either by activating the internal resistance of plants.
Other acquired or constitutive resistances are implied by the presence in the soil of certain antagonistic micro-organisms such as Pseudomonas spp fluorescens, Fusarium oxysporum etc. These micro-organisms reduce the severity of various soil-borne diseases in several ways:
With regard to the induction of resistance mechanisms in the plant, also known as "Induced Systemic Resistance" (ISR), it is interesting to cite the example of cucumbers. Strains of rhizobacteria were found to protect leaves against anthracnose caused by the fungus Colletotrichum orbiculare (9).
Studies have shown that resistance can also be a consequence of competition between micro-organisms to absorb nutrients from the soil. Pathogenic micro-organisms cannot compete with beneficial micro-organisms when the latter are predominant. In general, competition for nutrients is more intense in resistant soils than in susceptible soils, indicating that the amount of microbial biomass in the resistant soil plays an important role.
In constitutive resistance, the soil environment opposes the expression of the pathogenicity of the introduced or pre-existing infectious agent. In acquired resistance, the resistance is gradually built up year after year through the use of certain cultivation techniques or, more frequently, through repeated cultivation of the host plant on the same plot, which seems strange at first sight.
The biological resistance of soils to certain diseases has been demonstrated by the disappearance of this resistance in a soil sample when it is sterilised. Researchers at INRA have shown that there are 10 times more wild Fusarium spp. in a resistant soil from Châteaurenard than in the susceptible soil from Ouroux (Dt du Rhône), while the pathogen, Fusarium vascularis, is established at comparable levels in both soils. In the absence of a susceptible plant, the pathogen population changed little over time in both the resistant and susceptible soils and persisted for more than a year after its introduction. In the presence of a susceptible plant, the pathogen population tends to increase in susceptible soil in relation to the evolution of the disease (10)
Other acquired or constitutive resistances are implied by the presence in the soil of certain antagonistic micro-organisms such as Pseudomonas spp fluorescens, Fusarium oxysporum etc. These micro-organisms reduce the severity of various soil-borne diseases in several ways:
With regard to the induction of resistance mechanisms in the plant, also known as "Induced Systemic Resistance" (ISR), it is interesting to cite the example of cucumbers. Strains of rhizobacteria were found to protect leaves against anthracnose caused by the fungus Colletotrichum orbiculare (11).
Studies have shown that resistance can also be a consequence of competition between micro-organisms to absorb nutrients from the soil. Pathogenic micro-organisms cannot compete with beneficial micro-organisms when the latter are predominant. In general, competition for nutrients is more intense in resistant soils than in susceptible soils, indicating that the amount of microbial biomass in the resistant soil plays an important role.
In constitutive resistance, the soil environment opposes the expression of the pathogenicity of the introduced or pre-existing infectious agent. In acquired resistance, the resistance is gradually built up year after year through the use of certain cultivation techniques or, more frequently, through repeated cultivation of the host plant on the same plot, which seems strange at first sight.
1) Antoun et Kloepper, 2001
2) Sol : interface fragile P. Stengel, S. Gelin INRA 1998.
3) Loper, 1988 , Paulitz et Loper, 1991 , Dwivedi et Johri, 2003
4) La Mycorhize à arbuscules : quels bénéfices pour l’homme et son environnement dans un contexte de développement durable - Anissa Lounès-Hadj Sahraoui. Synthèse Revue des Sciences et de la Technologie N° 26 avril 2013 - Université Badji Mokhtar Annaba – Algérie.
5) Les champignons mycorhiziens arbusculaires et leur symbiose végétale
6) La symbiose mycorhizienne – une association entre les plantes et les champignons – Jean Carbaye (Directeur de recherche INRA)
7) Glomalin: Hiding Place for a Third of the World's Stored Soil Carbon - United States Department of Agriculture - AgResearch Magazine
8) Vivant et al. 2013
9) Plant growth-promoting rhizobacteria (PGPR): Their potential as antagonists and biocontrol agents – genetic and molecular biology – dec 2012 - Anelise Beneduzi , Adriana Ambrosini , and Luciane MP Passaglia
10) Recherches sur la résistance des sols aux maladies. IX. - Dynamique des populations du Fusarium spp. et de Fusarium oxysporum f. sp. melonis dans un sol résistant et dans un sol sensible aux fusarioses vasculaires - Claude ALABOUVETTE, Yvonne COUTEAUDIER Jean LOUVET Marie-Louise SOULAS I.N.R. A., Station de Recherches sur la Flore pathogène dans le Sol, Dijon – agronomie 1984
11) Vivant et all – 2013 ; signalé dans l’atlas français des bactéries du sol.
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